Ok, first off, this question is purely hypothetical. While it could happen, I highly doubt that it will.
With that said, let's say that one of the skill card decks is out of cards. The discard pile is also out of cards. The new FAQ says that if that's the case, no one draws any cards from that deck until some cards are discarded. First question: if the destiny deck has to be replenished while a deck is completely out, is that deck skipped?
Now, the next question. Let's say that one of the decks has only one card left in it (and no discards), and it's time to replenish the destiny deck again. Since there's only one card in one of the skill decks, the destiny deck will end up with 9 cards. Meaning, four skill checks later, there will be one card left in the destiny deck. When another skill check is drawn, is only one card added from the destiiny deck?